Neuroscience: How Meditation Transforms Brain Biochemistry and Structure
Meditative practices can increase brain thickness and prevent thinning, potentially changing brain structure and chemistry at the cellular, genetic, and systemic levels.
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Dear Readers,
I have been a bit quiet lately, busy working on exciting projects, including bringing on board some top-notch healthcare professionals as guest authors for my health and wellness newsletters. I am thrilled to share their expert insights with you soon.
In the meantime, I want to present a condensed version of a significant research piece I've been conducting over the last 30 years. This research has profoundly impacted my own health and well-being, and I’m eager to pass on what I’ve learned. Although I aimed to keep it concise, the complexity of the topic led to a longer read. Feel free to skim through if needed and focus on the key takeaways at the end—they are the heart of the message.
Though my background is rooted in technology and science, I am deeply drawn to metaphysics, mysticism, and spirituality — interests I explore for compelling reasons I have shared in previous stories.
After years of physical, mental, and emotional struggles in my younger life, I decided to become my own therapist. During my cognitive science studies, I learned that while we can’t directly observe the brain’s inner workings, advances in science and technology offer some insight into its structure, chemistry, and function. Yet, despite these breakthroughs, we still lack the ability to manipulate the brain directly.
We now understand that our thoughts, behaviors, and actions can indirectly improve brain function. This is where mindfulness and meditative practices become potent tools for boosting brain health, enhancing neurobiological performance, and sharpening cognitive function.
Through over three decades of mindfulness and meditation, I learned to leverage my thoughts, emotions, behaviors, and physical actions to positively impact the brain structure and improve cognitive abilities like working memory, procedural memory, attention, focus, task switching, intention, intuition, problem-solving, creativity, and decision-making.
I conducted countless experiments sensibly and methodically and even documented the distilled version of my convoluted and comprehensive mind gym in a story titled How I Train My Brain Daily for Mental Clarity and Intellectual Productivity, which went viral on multiple platforms due to its originality, authenticity, relatability, and memorability.
As a psychosomatic practice, meditation impacts more than just the mind; it has measurable effects on our neurobiology and overall spiritual and physical functioning. Studies I have reviewed suggest that meditation can even influence our genes, a topic I explored in a previous article. The genetic effects of meditation are a crucial part of my ongoing research, and I shall share more about these findings in future stories.
Despite facing challenges such as being banned from writing about my experiments in the UK and the US bulletin boards, I have been documenting the somatic experience of meditation since the early 1990s.
My recent story highlights how both science and metaphysics view meditation from a unified perspective. I have also covered practical steps to prevent cognitive decline and impairment, with meditation being a crucial practice for delaying mental deterioration and potentially extending both our lifespan and healthspan.
Why I wrote this critical story today with passion
In this short story, I want to distill my years of research into mindfulness and meditative practices and explain the mechanisms behind the physical effects of meditative practices on the brain at a high level, leveraging numerous insightful studies.
A growing body of knowledge sheds light on how meditation can reshape our brain’s structure and chemistry, which can delay the onset of dementia, which is a widespread neurodegenerative condition affecting the lives of millions with no cure yet.
Many studies related to mindfulness and meditative studies are scholarly, so it is very difficult for the public to comprehend them. Therefore, I want to keep my points relatable and down-to-earth by highlighting the role of neuroplasticity, where our brains can rewire and reorganize themselves based on our thoughts, emotions, experiences, and habits.
While the points discussed in this article are grounded in scientific research and theory, I have mainly used my decades of personal experience with meditation and observations of Zen masters in my circles to triangulate my empirical findings. To inform new readers, for many years, I have made meditation a consistent habit and lifestyle, practicing it thrice daily.
In earlier days, I was drawn to meditative practices after exploring their benefits in scholarly papers and clinical studies. Over time, I began to experience these positive effects firsthand, noticing how daily meditation improved various aspects of my life. Through these personal experiments, I have gained a deep appreciation for the transformative power of meditation and how it can enrich our daily lives and make us joyful and peaceful despite our challenges.
From a psychosomatic angle, a 2009 Study in Springer, titled The exploration of meditation in the neuroscience of attention and consciousness, informed that “meditation can be conceptualized as a family of complex emotional and attentional regulatory practices, in which mental and related somatic events are affected by engaging a specific attentional set.”
Researchers of the paper mentioned that “Many recent behavioral, electroencephalographic and neuroimaging studies have revealed the importance of investigating states and traits related to meditation to achieve an increased understanding of cognitive and affective neuroplasticity, attention and self-awareness for their possible clinical implications.”
Unlike previous wrong beliefs and claims, we now empirically know that the brain can grow at any age. Keeping it in growth mode by increasing BDNF, NGF, and other growth factors is an excellent way to delay the onset of neurodegenerative disorders like Alzheimer's disease by creating cognitive reserves.
My hypothesis is that The Brain Must Be in a Growth Mode to Prevent Neurological & Mental Health Issues. I will prove it one day with substantial empirical data. Stay tuned.
Without going into too many technical and scientific details, I want to provide a high-level overview of cortical thickness and thinning in the brain via neurobiological processes and share insights from the growing literature on meditation’s effects on the brain and the nervous system. First, I introduce meditation to those unfamiliar with the process at a very high level.
What Is Meditation and What It Is Not
Meditation has been practiced for thousands of years by different cultures and spiritual traditions, but you don’t need to follow any particular religion to benefit from it. It can also be done in a completely non-religious way.
Experts like Richard Davidson, Jon Kabat-Zinn, Sara Lazar, and Daniel Goleman have researched meditation and found two main styles: focused attention and open monitoring.
In focused attention, you concentrate on one thing, like your breath or an object, and keep your focus there. On the other hand, open monitoring is about paying attention to your thoughts, feelings, and sensations without reacting or judging them.
Mindfulness meditation, a type of open monitoring, helps you stay present by noticing what’s happening in your mind and body as it comes and goes. Contrary to common belief, “distraction” is not meditation, as it involves a lack of focus rather than intentional awareness and mindfulness.
Whether you choose focused attention or open monitoring, the goal is to sharpen your awareness and get better at understanding how your mind works. Most meditation practices involve sitting in a quiet space, getting comfortable, and focusing on simple mental exercises to calm your mind.
Like me, during meditation, some people achieve a state of heightened awareness and inner calm by directing their attention to a specific object, like the breath, a mantra, or a particular sensation. The goal is to let go of distracting thoughts and achieve deep concentration and stillness.
In general, people use meditation in their daily routines to promote well-being, reduce stress, improve attention, enhance self-awareness, and gain unique perceptions. But in the beginning, it can be very challenging as it stresses the brain like physical activities. Therefore, initially, meditation is not a stress management tool. However, it can significantly lower stress when it becomes a habit.
Studies like this in Cambridge Core, show that regular meditation practice can have benefits like reducing anxiety, improving emotional regulation, enhancing cognitive function, and promoting physical and mental relaxation during difficult times.
Meditation is increasingly used as a complementary practice in healthcare environments, like mindfulness-based therapies, to support mental and emotional well-being. It is also helpful to sleep better. After meditation practices, my sleep significantly improved. I also documented a case study of a friend who solved her sleep issues with meditation.
What Does Meditation Do to the Brain Physically?
Let me start by explaining some key brain areas that meditation can affect. One important part of the brain is the cortex, which is made up of layers of neurons.
These layers help process what we see, hear, and feel, control how we move, and support higher-level thinking. The thickness of the cortex, called “cortical thickness,” is a measure linked to brain development, mental flexibility (neuroplasticity), and overall brain health.
Cortical thickness refers to how thick or deep the brain's outer layer (the cerebral cortex) is. This part of the brain manages important functions like attention, memory, perception, and language. While the thickness of the cortex differs from person to person due to genetics, age, and life experiences, thicker areas of the cortex are often connected to stronger cognitive abilities and better mental health.
On the flip side, “cortical thinning” means the cortex is becoming thinner, which naturally happens as we age. Stress, certain neurological conditions, and lifestyle choices can speed this up. When thinning happens in specific brain parts, it can affect how well we think and remember, depending on which areas are involved.
While some thinning is normal as we age, too much thinning can be a warning sign of issues like Alzheimer’s or other forms of dementia..It can also show up in people with mental health challenges, such as depression or schizophrenia.
Understanding how and why cortical thinning happens helps scientists learn more about brain aging and conditions that affect mental health. Current research is working to find ways to keep our brains healthy and reduce the risks of cognitive decline as we age.
This valuable study, published in Neuroreport in 2006 as a pioneer in meditation research in neuroscience, informed previous research indicating that long-term meditation practice was associated with altered resting electroencephalogram patterns, suggesting long-lasting changes in brain activity.
They hypothesized that “meditation practice might be associated with changes in the brain’s physical structure. Magnetic resonance imaging assessed cortical thickness in 20 participants with extensive Insight meditation experience, which involved focused attention to internal experiences.”
They found that “brain regions associated with attention, interception, and sensory processing were thicker in meditation participants than in matched controls, including the prefrontal cortex and right anterior insula.”
“Between-group differences in prefrontal cortical thickness were most pronounced in older participants, suggesting that meditation might offset age-related cortical thinning. The thickness of the two regions correlated with the meditation experience. These data provided the first structural evidence for experience-dependent cortical plasticity associated with meditation practice.”
Recent studies such as distilled Neuroscience.com indicate that meditation can impact cortical thickness in regions involved in attention, self-awareness, interoception, and sensory processing, which are important for our well-being.
Despite years of investigation, the specific mechanisms underlying the effects of meditation on cortical thickness are still not fully understood. Therefore, we need more research to understand the relationship entirely and take protective measures. I believe some well-designed clinical studies with large populations could shed light on this matter.
A 2023 study in Springer titled Cortical thickness is related to cognitive-motor automaticity and attention allocation in individuals with Alzheimer’s disease: a regions of interest study mentioned “a distinct pattern of cortical thinning and resultant changes in cognition and function characterizes Alzheimer’s. These result in prominent deficits in cognitive-motor automaticity.”
After reading many studies like that, I learned that the key points and concepts in the literature are neuroplasticity, neurogenesis, stress reduction, self-regulation, enhanced attention, improved memory, emotional regulation, and lowered mind-wondering. I want to touch on these critical points briefly with summaries of some valuable studies.
Cognitive science studies suggest that meditation might stimulate neurogenesis, the birth of new neurons, particularly in the hippocampus, increasing gray matter density. Increased neurogenesis in the hippocampus might contribute to changes in cortical thickness.
Based on studies conducted until 2015, researchers found that meditation can trigger neurotransmitters that modulate psychological disorders like anxiety. This 2015 study reviewed the psychological effects of meditation, the role of neurotransmitters, and studies using EEG and fMRI.
For example, this magnetoencephalography study in 2018 informed that “mindfulness meditation is related to long-lasting changes in hippocampal functional topology during a resting state.”
These studies indicate that meditation can induce neuroplasticity (the brain’s ability to change and reorganize itself) and that regular meditation practice might lead to structural changes in the brain, increasing its cortical thickness.
The thicker cortex facilitates stronger neural connections, enhancing the coordination and communication between brain areas (the prefrontal and parietal cortexes) involved in attention. Greater cortical thickness in the prefrontal cortex has been associated with better attentional control and the ability to sustain focus.
Greater cortical thickness in the hippocampus is linked to better memory performance, particularly in tasks involving acquiring and retrieving new information. It indicates a more significant number of neurons, synapses, and dendritic connections, which support the formation and storage of memories. Thinning hippocampus indicates disorders.
Cortical thickness can affect the distribution and availability of neurotransmitters. The density and balance of therapeutic neurotransmitters influence cognitive processes.
Cortical thickness is influenced by synaptic density, which refers to the number and strength of connections between neurons. Greater synaptic density in specific cortical regions can enhance the neural networks involved in attention and memory processes.
Myelin (a fatty substance that wraps nerve fibers) is crucial in neural transmission. Thicker cortical regions have higher myelination, enabling faster communication between neurons. According to a hypothesis, “frontal theta induced by meditation produces a molecular cascade that increases myelin and improves connectivity.”
This 2009 study in the Journal of Neurosciences conducted three months of intensive meditation training. “Meditation reduced variability in attentional processing of target tones, indicating enhanced theta-band phase consistency of oscillatory neural responses over anterior brain areas and reduced reaction time variability.”
Mindfulness and meditation practices involve relaxation and stress reduction. We now know that oxidative stress can adversely affect the brain, including the shrinkage of brain regions. By reducing stress levels, meditation might promote the preservation or growth of cortical thickness.
I want to touch on mind wandering. It is spontaneous, uncontrolled thoughts associated with cortical thinning. From my experience and observations, meditation can lower mind wandering. By enhancing attentional control and reducing mind wandering, meditation might contribute to preserving cortical thickness. I also found evidence in the literature.
For example, this 2020 review study provided a theoretical framework highlighting the neurocognitive mechanisms by which contemplative practices influence the neural and phenomenological processes underlying random thoughts, which include mind-wandering, dreaming, and creative thinking.
The paper informed that “Mind-wandering in the context of meditation provides individuals a unique and intimate opportunity to closely examine the nature of the wandering mind, cultivating an awareness of ongoing thought patterns while simultaneously cultivating equanimity and compassion towards the content of thoughts, interpretations, and bodily sensations.”
Clinical trials such as those documented in the Frontiers in 2019 titled Brief Mindfulness Meditation Improves Emotion Processing show mindfulness meditation can improve emotion processing. Some of those studies link emotional regulation to cortical thickness, as I covered earlier.
One outstanding 2022 paper published on Social Cognitive and Affective Neuroscience titled Prefrontal cortical thickness, emotion regulation strategy use and COVID-19 mental health” stated that “Momentary emotion regulation strategy use mediated the association between cortical thickness in right lateral prefrontal cortex assessed before the pandemic and mental health during the pandemic.”
Conclusions and Key Takeaways
Many research studies show that meditation can increase cortical thickness in brain areas related to attention, sensory processing, and self-awareness. This effect is especially noticeable in older adults, suggesting meditation may help slow down age-related cortical thinning.
The thickening of these regions is linked to better attention control and improved memory. Meditation also supports neuroplasticity — the brain’s ability to adapt and reorganize — and encourages neurogenesis, the growth of new neurons, particularly in the hippocampus, a critical area for learning, memory, and emotional balance.
By strengthening these brain regions, meditation enhances the connections between areas responsible for attention and memory. It also reduces stress, curbs mind-wandering, and promotes emotional regulation, all of which may help maintain cortical thickness and protect cognitive abilities.
The growing body of evidence provides strong support for the role of meditation in preserving brain health and cognitive function, making it a powerful tool for mental and emotional well-being.
Based on my decades of experience meditating several times daily, I can offer the following tips for you to consider and tailor to your needs, goals, and aspirations.
1 — Meditation is personal. There’s no one-size-fits-all approach, so find what works for you. Some people may struggle to meditate, and that’s okay — don’t pressure yourself into it if it doesn’t feel right. Be patient, flexible, and kind to yourself. It is not religion or science.
2 — Start small to avoid overwhelm. Meditation can initially feel mentally demanding, so begin with short sessions, like 5–10 minutes. Gradually increase the time as your mind adjusts, and you feel more comfortable.
3 — Consistency is vital. To truly benefit from meditation, make it part of your daily routine. Whether it’s morning, evening, or during a break, stick to a schedule that fits your lifestyle and helps create a lasting habit.
4 — Use your breath as your guide. Focusing on your breath is an easy and effective way to anchor your attention. When distractions come, simply notice them, then gently return your focus to your breathing.
5—Observe without judgment. Practice acknowledging your thoughts and feelings without reacting to them. Let them flow in and out naturally, cultivating a nonjudgmental awareness.
6 — Try different styles. Meditation comes in many forms. Whether chanting, using mantras or visualizing, explore different techniques to find what resonates with you and addresses your needs.
7 — Keep an open mind. Believe in the benefits of meditation as there is significant empirical evidence. It is not pseudo-science. Adopting an optimistic, open attitude will help you welcome the practice and get the most out of it for your mental and emotional well-being.
8 — Appreciate yourself. Take moments to thank your body and mind for allowing you to meditate. Practice self-compassion and recognize the value of this time dedicated to nourishing yourself. It’s an act of self-love, and you deserve it.
9 — Meditation isn’t for everyone, and that’s okay. While many benefit from it, some may face challenges due to health conditions or unique brain patterns. It’s vital to listen to yourself — don’t push through discomfort just to fit into a practice. Meditation and Mindfulness Are Not as Simple as They May Seem in Theory.
10 — Explore alternatives if needed. If traditional meditation feels unsettling or stressful, there are other practices that can support mindfulness and well-being. Seek guidance from professionals if necessary, and always respect your limits.
11— There’s no one right way. Meditation is about personal growth, not rigid rules or specific outcomes. It’s meant to bring peace, clarity, and self-awareness in a way that suits your journey. Embrace what works for you, and let go of the pressure to conform.
12— Honor your well-being above all. The ultimate goal of meditation, or any practice, is to encourage a sense of inner peace and balance. Whether through alternative methods or traditional routes, prioritize what brings you harmony and supports your physical and mental health.
Here is why I meditate three times daily. I also enjoy doing daily activities such as mindfulness practices and leveraging the meditative power of neurobics, which can also rewire the brain and prevent cognitive decline. Here’s How I Train My Brain Daily for Mental Clarity and Intellectual Productivity.
Thank you for reading my perspectives. I wish you a healthy and happy life.
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Health and Wellness by Dr Mehmet Yildiz
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I read this story before and after publishing. I had to remove some scientific details to make it more digestible but they were like killing my darling as they were important. Thank you for sharing your valuable research, experiences, and insights so passionately. I also love meditation which saved my life. I'd be delighted to be a guest author for your health and well being newsletters especially for complex scientific topics related to health health sciences and healthcare where I spent 53 years of my life. Thank you for the invitation as guest author and editor of your esteemed publications.🙏 I feel honored.
Meditation is the basis of a healthy life and progress.
We are too "in the head." It is necessary to enter your silence and descend into the body.
Thanks for sharing, Dr. Mehmet!